Method for the determination of the dna methylation level of a cpg position in identical cells within a tissue sample

ABSTRACT

Aspects of the present invention relate to the determination of the DNA methylation level at one or more CpG position within cells of a defined type in a tissue sample. This methylation level is deduced from the total DNA methylation level of all cells of the sample and from the content of said cells of interest. In aspects of the invention, the cell content is determined by means of histopatholoy, staining methods, antibodies, expression analysis or DNA methylation analysis.

CROSS-REFERENCE TO RELATED APPLICATIONS

The present application is a continuation of U.S. patent applicationSer. No. 12/085,212, inventors Lewin et al., filed May 19, 2008, which,in turn, is a 371 of PCT Application No. PCT/EP2006/011377, filed Nov.17, 2006, the disclosures of both of which are incorporated herein byreference.

FIELD OF THE INVENTION

The invention relates generally to novel and substantially improvedmethods for the determination of the DNA methylation level of cells of asubpopulation of cells within a heterogeneous sample.

BACKGROUND OF ASPECTS OF THE INVENTION

Many diseases, in particular cancer diseases, are accompanied by amodified gene expression. This may be a mutation of the genesthemselves, which leads to an expression of modified proteins or to aninhibition or overexpression of the proteins or enzymes. A modulation ofthe expression may however also occur by epigenetic modifications, inparticular DNA methylation. Such epigenetic modifications do not affectthe actual DNA coding sequence. It has been found that DNA methylationprocesses have substantial implications for the health, and it seems tobe clear that knowledge about methylation processes and modifications ofthe methyl metabolism and DNA methylation are essential forunderstanding diseases, for the prophylaxis, diagnosis and therapy ofdiseases.

The precise control of genes, which represent a small part only of thecomplete genome of mammals, is a question of the regulation underconsideration of the fact that the main part of the DNA in the genome isnot coding. The presence of such trunk DNA containing introns,repetitive elements and potentially actively transposable elements,requires effective mechanisms for their durable suppression (silencing).Apparently, the methylation of cytosine by S-adenosylmethionine (SAM)dependent DNA methyltransferases, which form 5-methylcytosine,represents such a mechanism for the modification of DNA-proteininteractions. Genes can be transcribed by methylation-free promoters,even when adjacent transcribed or not-transcribed regions are widelymethylated. This permits the use and regulation of promoters offunctional genes, whereas the trunk DNA including the transposableelements is suppressed. Methylation also takes place for the long-termsuppression of X-linked genes and may lead to either a reduction or anincrease of the degree of transcription, depending on where themethylation in the transcription unit occurs.

Almost all DNA methylation in mammals is restricted tocytosine-guanosine (CpG) dinucleotide palindrome sequences, which arecontrolled by DNA methyl transferases. CpG dinucleotides are about 1 to2% of all dinucleotides and are concentrated in so-called CpG islands. Agenerally accepted definition of CpG islands is an at least 200 bp longDNA region with a CpG content of at least 50%, and wherein the ratio ofthe number of observed CG dinucleotides and the number of the expectedCG dinucleotides is larger than 0.6 (Gardiner-Garden, M., Frommer, M.(1987) J. Mol. Biol. 196, 261-282; incorporated by reference in itsentirety). Typically, CpG islands have at least 4 CG dinucleotides in asequence having a length of 100 base pairs.

If CpG islands are present in promoter areas, they often have aregulatory function over the expression of the respective gene. Ingeneral if the CpG island is hypomethylated, expression can take place.Hypermethylation often leads to the suppression of the expression. Inthe normal state, a tumor suppressor gene is hypomethylated. If ahypermethylation takes place, this will lead to a suppression of theexpression of the tumor suppressor gene, which is frequently observed incancer tissues. In contrast thereto, oncogenes are hypermethylated inhealthy tissue, whereas in cancer tissue they are frequentlyhypomethylated.

Due to the methylation of cytosine, the binding of proteins regulatingthe transcription is often prevented. This leads to a modification ofthe gene expression. With regard to cancer for instance, the expressionof cell division regulating genes is often affected, e.g. the expressionof apoptosis genes is regulated down, whereas the expression ofoncogenes is regulated up. The hypermethylation of the DNA also has along-term influence on the regulation. By the methylation of cytosine,histone de-acetylation proteins can bind by their5-methylcytosine-specific domain to the DNA. This has as a consequencethat histones are de-acetylated, which will lead to a tighter compactingof the DNA. Thereby, regulatory proteins do not have the possibilityanymore to bind to the DNA.

For this reason, the accurate determination of DNA methylation levels isvery important. A tailored therapy for the respective person can then bedetermined. Also the effects of a therapy can be monitored. Moreover theaccurate detection of DNA levels is also an important tool fordeveloping new approaches for the prevention, diagnosis and treatment ofdiseases and for the screening for targets.

Therefore a great technical need exists for highly accurate methods fordetermining the exact methylation level of cytosines, which aremethylated in a disease-specific manner. The present invention makessuch a method available. The method according to the invention is morepowerful than prior art methods.

An overview for detecting 5-methylcytosine may be gathered from thefollowing review article: Fraga F M, Esteller M, Biotechniques 2002September, 33(3):632, 634, 636-49 (hereby incorporated by reference inits entirety). The most common methods are based on the use ofmethylation sensitive restriction enzymes capable of differentiatingbetween methylated and unmethylated DNA and on the treatment withbisulfite.

A method, which is based on the use of methylation sensitive restrictionenzymes for determining methylation, is the Differential MethylationHybridization (DMH, [Huang et al, Hum Mol Genet, 8:459-470, 1999; U.S.patent application Ser. No. 09/497,855] both of these cited referencesare incorporated by reference to their entirety). According to thismethod, DNA is initially cut with a single non-methylation-specificrestriction enzyme, for instance MseI. The obtained fragments are thenligated with linkers. The thus obtained mixture of fragments is then cutwith methylation-specific endonucleases, for instance BstUI and/orHpaII, and amplified by means of linker-mediated PCR. The above stepsare performed on the one hand with DNA from a diseased tissue and on theother hand with DNA from adjacent healthy tissue of the same tissuetype, and the respectively obtained fragments are labeled with differentfluorescence dyes. Both fragment solutions are then co-hybridized on aCpG island microarray. The pattern of fluorescent dots visible thereincan then be analyzed to find out, for which CpG clones there aredifferences in the methylation. As a supplement with regard to thetechnology and methodological details, reference is made to thedocuments WO03/087774 and U.S. Pat. No. 6,605,432 (both of these citedreferences are incorporated by reference to their entirety).

But, in general, the use of methylation sensitive enzymes is limited dueto the selectivity of the restriction enzyme towards a specificrecognition sequence.

Therefore, the treatment with bisulfite, allowing for the specificreaction of bisulfite with cytosine, which, upon subsequent alkalinehydrolysis, is converted to uracil, whereas 5-methylcytosine remainsunmodified under these conditions (Shapiro et al. (1970) Nature 227:1047; hereby incorporated by reference in its entirety)) is currentlythe most frequently used method for analyzing DNA for 5-methylcytosine.Uracil corresponds to thymine in its base pairing behavior, that is ithybridizes to adenine; whereas 5-methylcytosine does not change itschemical properties under this treatment and therefore still has thebase pairing behavior of a cytosine, that is hybridizing with guanine.Consequently, the original DNA is converted in such a manner that5-methylcytosine, which originally could not be distinguished fromcytosine by its hybridization behavior, can now be detected as the onlyremaining cytosine using “normal” molecular biological techniques, forexample, amplification and hybridization or sequencing. All of thesetechniques are based on base pairing, which can now be fully exploited.

In patent application WO05/038051 (hereby incorporated by reference inits entirety) improvements for the conversion of unmethylated cytosineto uracil by treatment with a bisulfite reagent are described. Accordingto this method the reaction is carried out in the presence of aaliphatic cyclic ether (e.g. dioxane) or in the presence of a n-alkyleneglycol compound (e.g. diethylene glycol dimethyl ether). The bisulfiteconversion is conducted at a temperature in the range of 0-80° C. with 2to 5 thermo-spikes (brief incubation at increased temperature of 85-100°C.).

Subsequent to a bisulfite treatment, usually short, specific fragmentsof a known gene are amplified and either completely sequenced (Olek A,Walter J. (1997) The pre-implantation ontogeny of the H19 methylationimprint. Nat Genet. 3: 275-6; hereby incorporated by reference in itsentirety) or individual cytosine positions are detected by a primerextension reaction (Gonzalgo M L and Jones P A. (1997) Rapidquantitation of methylation differences at specific sites usingmethylation-sensitive single nucleotide primer extension (Ms-SNuPE).Nucleic Acids Res. 25:2529-31, WO 95/00669; both of these citedreferences are incorporated by reference in its entirety) or byenzymatic digestion (Xiong Z, Laird P W. (1997) COBRA: a sensitive andquantitative DNA methylation assay. Nucleic Acids Res. 25: 2535-4;hereby incorporated by reference in its entirety).

Another technique to detect the methylation status is the so-calledmethylation specific PCR (MSP) (Herman J G, Graff J R, Myohanen S,Nelkin B D and Baylin S B. (1996), Methylation-specific PCR: a novel PCRassay for methylation status of CpG islands. Proc Natl Acad Sci USA. 93:9821-6; hereby incorporated by reference in its entirety). The techniqueis based on the use of primers that differentiate between a methylatedand a non-methylated sequence applied after bisulfite treatment of saidDNA sequence. The primer either contains a guanine at the positioncorresponding to the cytosine in which case it will after bisulfitetreatment only bind if the position was methylated. Alternatively theprimer contains an adenine at the corresponding cytosine position andtherefore only binds to said DNA sequence after bisulfite treatment ifthe cytosine was unmethylated and has hence been altered by thebisulfite treatment so that it hybridizes to adenine. With the use ofthese primers, amplicons can be produced specifically depending on themethylation status of a certain cytosine and will as such indicate itsmethylation state.

A further technique is the detection of methylation via a labelledprobe, such as used in the so-called Taqman PCR, also known asMethyLight™ (U.S. Pat. No. 6,331,393; hereby incorporated by referencein its entirety). With this technique it became feasible to determinethe methylation state of single or of several positions directly duringPCR, without having to analyze the PCR products in an additional step.

In addition, detection by hybridization has also been described (Olek etal., WO 99/28498; both of these cited references are incorporated byreference to their entirety).

The quantification of methylation, e.g. a quantitative detection of theDNA methylation level or the amount of methylated or unmethylated DNA,is possible according to the state of the art by several methods (Laird,P. Nat Rev Cancer 2003; 3(4):253-66.; hereby incorporated by referencein its entirety). These methods are usually based on bisulfite treatmentand subsequent amplification. In most cases the analysis takes placeafter the amplification (e.g. Ms-SNuPE, hybridisation on microarrays,hybridisation in solution or direct bisulfite sequencing; for review:Fraga and Esteller 2002, loc. cit.; hereby incorporated by reference inits entirety). However, this “endpoint analysis” leads to severalproblems; e.g. product inhibition, enzyme instablity and decrease of thereaction components, with the result that the amplification does notproceed uniformly. Therefore a correlation between the amount of inputDNA and the amount of amplificate does not always exist. As aconsequence, the quantification is error-prone (for review: Kains: ThePCR plateau phase—towards an understanding of its limitations. Biochem.Biophys. Acta 1494 (2000) 23-27; hereby incorporated by reference in itsentirety).

The real time PCR based MethyLight™ technology uses a different approachfor a quantification (for review U.S. Pat. No. 6,331,393; herebyincorporated by reference in its entirety). In brief, this methodanalyses the exponential phase of the amplification instead of theendpoint. Traditionally a threshold cycle number (Ct) is calculated fromthe fluorescence signal that describes the exponential growth of theamplification (P S Bernard and C T Wittwer, Real-time PCR technology forcancer diagnostics, Clinical Chemistry 48, 2002; hereby incorporated byreference in its entirety). The Ct value is dependent on the startingamount of methylated DNA. By comparing the Ct value of an experimentalsample with the Ct value of a standard curve the methylated DNA can bequantified (for review: Trinh et al. 2001, loc. cit.; Lehmann et al.:Quantitative assessment of promoter hypermethylation during breastcancer development. Am J Pathol. 2002 February; 160(2):605-12; both ofthese cited references are incorporated by reference to their entirety).

There are two commonly used methods to calculate the Ct value. Thethreshold method selects the cycle when the fluorescence signal exceedsthe background fluorescence. The second derivative maximum methodselects the cycle when the second derivative of the amplification curvehas its maximum. For classical real-time PCR assays both methods produceidentical results.

However, both methods do not produce exact results for thequantification of methylation via MethyLight™ assays. The MethyLight™technology normally uses a methylation specific amplification (bymethylation specific primers or blockers, sometimes methylationunspecific primers are used) combined with a methylation specific probe(for review: Trinh et al., 2001, loc. cit.; hereby incorporated byreference in its entirety). The methylation specific probe results influorescence signals from only a part of the generated amplificatesdepending on the methylation status of the CpG positions covered by theprobe. This results in amplification curves that are downscaled comparedto curves from completely methylated template DNA. These downscaledcurves are the reason that both analysis methods generate incorrectresults.

The threshold method assumes that all curves are in their exponentialgrowth phase when exceeding the threshold. However, for samples with lowproportions of DNA that is methylated at the probe (especially common incancer diagnostics) this is not true. Amplification curves are alreadyin the plateau phase and Ct estimation will be wrong.

The second derivative maximum method is independent from the overallintensity of the amplification curve. It only takes the shape intoaccount which corresponds to a quantification of DNA that is methylatedat the priming sites. The information generated by the methylationspecific probe—represented by the signal intensity—is not used.

An improved method is the MethyLight™ ALGO™ method (EP 04090255.3;hereby incorporated by reference in its entirety), which is based on theMethyLight™ technology. According to this improved method, the degree ofmethylation is calculated from the signal intensities of probes usingdifferent algorithms.

A further method is the so-called QM™ assay (for reviewPCT/EP2005/003793, hereby incorporated by reference in its entirety),which is also based on real-time PCR. According to this method, anon-methylation-specific, conversion-specific amplification of thetarget DNA is produced. The amplificates are detected by means of thehybridization of two different methylation-specific real-time PCRprobes. One of the probes is specific for the methylated state, whilethe other probe is specific for the unmethylated state. The two probesare labelled with different fluorescent dyes. The quantification of thedegree of methylation can be carried out during specific PCR cycles byemploying the ratio of signal intensities of the two probes.Alternatively, the Ct values of two fluorescent channels can also bedrawn on for the quantification of the methylation. In both cases,quantification of the degree of methylation is possible without thenecessity of determining the absolute DNA quantity. A simultaneousamplification of a reference gene or a determination of PMR values isthus not necessary. In addition, the method supplies reliable values forboth large and small DNA quantities as well as for high and low degreesof methylation.

The third preferred method for quantitative detection of DNA methylationis the so-called restriction assay, also known as Mest evaluation(PCT/DE205/001109; hereby incorporated by reference in its entirety). Inbrief, according to this method, DNA is digested with at least onemethylation-specific restriction enzyme. After this, the digested DNA issubjected to real time PCR amplification. But amplificates are onlyamplified from said DNA if the DNA was not previously cut by themethylation-specific enzyme or enzymes within the sequence of theamplificate. The percentage of methylated DNA is then deduced bycomparison of the signal intensity obtained for the sequence of interestwith that of a reference sample.

According to the said methods, a quantification of methylation levels ispossible. But recent studies have shown, that they only have a limitedaccuracy making a precise characterization of samples very difficult.Therefore the differentiation, grading, and staging of diseased tissueis impaired and therefore also the diagnosis of proliferative disordersor predisposition to those.

Because of that, it is the technical object of the invention to providea quantitative method for DNA methylation analysis which has a higheraccuracy than the known methods. Consequently, a liable differentiation,grading, and staging of diseased tissue and therefore also the diagnosisof proliferative disorders or predisposition to those is enabled.

Very surprisingly, this technical need can be fulfilled by a simpleapproach according to the invention. The present invention addresses theproblem, heretofore unrecognized, that the majority of biologicalsamples isolated from a patient are a heterogenous mixture of aplurality of pathologically cell types e.g. healthy tissue and diseasedtissue. The method of the invention enables the quantification ofselected tissue or cellular type(s) within said heterogenous biologicalsample. Said method is particularly useful in the field of pathologywherein a biological sample from a patient is often a heterogeneousmixture of healthy and sick cells. By enabling the quantification of theamount of healthy and sick cells within a sample the invention assistsin the quantification of disease markers within said sample.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1 and 2 each provide a matrix of the quantified methylation valueof genomic CpG positions as measured by means of DMH according toExample 1. Each row of a matrix represents a DMH fragment and eachcolumn represents an individual DNA sample. The degree of methylationrepresented by the shade of each position within the column from blackrepresenting 100% methylation to light grey representing 0% methylation.‘A’ indicates normal tissue, ‘B’ indicates surgically removed lungcancer samples and ‘C’ indicates lung cancer cell lines.

FIG. 3 provides a plot of the average methylation of 20 DMH fragments(SEQ ID NO: 21 to SEQ ID NO: 40) which are hypermethylated in lungcancer cell lines (X-axis), against 20 DMH fragments (SEQ ID NO: 1 toSEQ ID NO: 20) which are hypomethylated in lung cancer cell lines(Y-axis) as measured in 20 surgically removed lung cancer samplesaccording to Example 1.

FIG. 4 provides a plot of the pathologist estimated % tumour content(X-axis), against average methylation of 20 DMH fragments (SEQ ID NO: 1to SEQ ID NO: 20) which are hypomethylated in lung cancer cell lines(Y-axis) as measured in 20 surgically removed lung cancer samplesaccording to Example 1.

FIG. 5 provides a plot of the pathologist estimated % tumour content(X-axis), against average methylation of 20 DMH fragments (SEQ ID NO: 21to SEQ ID NO: 40) which are hypermethylated in lung cancer cell lines(Y-axis) as measured in 20 surgically removed lung cancer samplesaccording to Example 1.

DETAILED DESCRIPTION OF ASPECTS OF THE INVENTION

For achieving the technical object, the invention teaches a method forthe determination of the DNA methylation level of one or more specificCpG positions of a subpopulation of cells within a tissue sample. Themethod comprises a) the determination of the cell content of asubpopulation of cells within the sample, b) the measurement of thetotal DNA methylation level of said one or more specific CpG positionswithin the tissue sample, c) determination of the DNA methylation levelwithin cells of said subpopulation of cells form the total DNAmethylation level of said one or more specific CpG positions within thetissue sample and the cell content of said subpopulation of cells withinthe tissue sample.

The central idea of the present invention is to consider samples takenfrom tumor tissue no longer as homogeneous as it is done according tomethods of the state of the art. Instead, according to the invention,only cells which really contributed to the state of interest of thediseased tissue are taken into account. Other cells always also part ofthe tumor are excluded from analysis. Of course, this central idea isnot limited to tumor tissue, it can be also transferred to anyquantitative analysis of DNA methylation, wherein the sample to beanalysed might be hetereogeneous.

Advantages of the Invention

The method of the invention has the following advantages: It has ahigher specificity, a higher reliability and a higher reproducibilitythan the so far known methods according to the state of the art.

The reason for this is that the methods of the state of the art considera sample taken from a tumor as homogeneous. According to them, everycell within a sample is thought to comprise the same tumor specificchanges in DNA methylation.

However, the amount of cells which are really specific for the tumor,its stage, grade, or differentiation is varying depending on numerousfactors such as the tumor type, or the stage, grade, differentiation andorigin of the tumor. According to the invention only cells of a singletype are taken into consideration which really contribute to the stateof interest of the diseased tissue. This leads to an improved accuracybecause the method of the invention is based on the known methods forDNA methylation analysis. The higher accuracy is thereby accompanied bya improved reliability and an improved reproducibility.

Moreover, the higher accuracy has the additional advantage that tumorscan even be analysed which comprise only a small number of altered cellsdistributed over a large area, for example liposarcoma, adeno carcinomaor Morbus Hodkin. This has so far not or only to a limited extent beenpossible with the known methods of the state of the art.

Of course, the method of the invention can in general be addressed toother problems, in which the DNA methylation of at least two differentsubpopulation of cells is mixed to various degrees.

Embodiments of the Invention

A preferred embodiment of the invention is a method for thedetermination of the DNA methylation level of one or more specific CpGpositions of a subpopulation of cells within a tissue sample, comprising

a) a determination of the cell content of said subpopulation of cellswithin the tissue sample in a quantitative or semiquantitative manner,b) measuring the total DNA methylation level of said one or morespecific CpG positions within the tissue sample, andc) determining the DNA methylation level within the cells of saidsubpopulation of cells from the total DNA methylation level of said oneor more specific CpG positions within the tissue sample and the cellcontent of said subpopulation of cells within the tissue sample.

The term “methylation level” represents hereby the quantitativelydetermined, average occupancy of methylcytosine at a single CpGdinucleotide in the genome across an entirety of DNA molecules(Siegmund, K D, Laird, P W. Methods 2002; 27(2):170-8.; herebyincorporated by reference in its entirety). According to the invention,it is possible to determine more than one different methylation levelssimultaneously. The entirety of DNA molecules is hereby defined in thatit is derived from the genome of cells which belong all to the same typeof cells herein referred as single cell type.

The tissue sample can be any kind of sample derived from a human being.Preferably the tissue sample is a biopsy or surgical sample derived froma tissue. It can also be preferably a remote sample such as sputum,stool or any bodily fluid, in particular serum, plasma, whole blood,saliva, urine, fluids from the pleural or peritoneal cavity,cerebrospinal fluid or a smear from a epithelial surface. Of course,also samples which are enriched with regard to a certain type or typesof cells are also preferably used for the method according to theinvention. In general, the sample can be treated in different ways foruse in the method of the invention. For example fresh, fresh frozen orarchived samples such as paraffin-embedded and/or formalin-fixed samplesare useable. Of course, samples treated differentially are also useableas long as the enable at least one of the embodiments of the inventionfor determining the cell content of a subpopulation of cells or the DNAmethylation analysis.

According to a preferred embodiment of the invention, the content ofcells of a subpopulation of cells is determined by means of stainingmethods, in particular by means of standard histotechnologic methods.Numerous suitable methods are well known to those with ordinary skillsin the art. A rough overview could be gained from the followingliterature: Burck, H C. Histologische Technik: Leitfaden für dieHerstellung mikroskopischer Präparate in Unterricht and Praxis. 6.edition, Thieme, 2002; Kiernan, J A. Histological and histochemicalmethods: theory and practice. 2. edition, Arnold Publishers, 1990;Ackermann and Rosai (editors). Surgical pathology. 9. edition, Mosby,2004; Killeen, A A. Principles of Molecular Pathology. Humana Press,2003; Romeis, B. Mikroskopische Technik. R. Oldenbourg Verlag, 1968 (allof these cited references are incorporated by reference to theirentirety). But many more staining methods are known in the art and maybe used according to the invention.

In a preferred embodiment, the cell content of a subpopulation of cellsis determined by means of the following stainings:

-   -   Hematoxilin/Eosin stain, a universal staining method for the        demonstration of nuclear features (stained by Hematoxilin in        blue) and cytoplasm (stained by Eosin in red).    -   Papadopulos stain, a standard staining used in cervical        cytology. It allows best to differentiate squamous cells from        different layers of the portio and their transformations.    -   Histochemical protocols that allow the specific labeling of        tissues components. Numerous of such methods are known to those        with ordinary skills in the art. Exemplary, only the Giemsa        Stain (nuclear features), the Elastica-van Gieson Stain        (connective tissue), the Ladewig Stain (connective tissue), and        the Tri PAS Stain (mucus) are listed here.

Further suitable stainings are

-   -   Perjodic Schiff Acid (PAS) Stain, which demonstrates glycogen        and neutral mucosubstances. It further outlines basement        membranes and is useful for the demonstration of the        intracytoplasmic crystals in alveolar soft part sarcoma.    -   Argentaffin and argyrophilic stains. The staining with        argentaffin depends on the presence of a substance in the        tissue. Many times, such a substance comprises a phenolic group        that reduces silver and other metallic salts. Examples for said        substance are catecholamines or indolamines. A popular protocol        for an argentaffin/argyrophilic stain is the staining of        paraffin sections according to the Fontana-Masson stain. In        general, silver stains are mainly used for the identification of        neuroendocrine cells and their tumors. But they can also be used        for the demonstration of reticulin fibers, melanin and calcium.    -   Amyloid stains, of which numerous methods are know to those        skilled in the art. Exemplary, only the Congo Red Stain is        mentioned. This staining allows the examination with standard as        well as polarized light. It is regarded as the most reliable and        practical technique to detect amyloid.    -   Reticulin stains, which demonstrate both reticular fibers and        basement membrane material. Reticular fibers consist of very        thin fibers of mainly type II collagen, which are widespread in        connective tissue throughout the body. Basement membranes are        largely composed of type IV collagen and laminin. Numerous        reticulin stains are known in the art. Exemplary reticulin        stains, in particular the Gomori's Stain, the Wilder's Stain,        the Gordon Stain, and the Sweets Stain are mentioned. Preferably        this stains are used in tumor pathology to distinguish the        following: i) epithelial from non epithelia neoplasms, ii)        various mesenchymal neoplasms from each other, and iii) in situ        from invasive carcinoma.    -   Further stains are for example staining methods for hemosiderin,        such as the Perls Stain, or for calcium, such as the von Kossa        Stain. According to the Perl's Stain, hydrochloric acid splits        off the protein bound to the iron allowing the potassium        ferrocyanide to combine specifically with the ferric ion to form        ferric ferrocyanide also known as Prussion blue. In the von        Kossa staining method, calcium is substituted by silver in        calcium salts. The silver salt is then reduced to black metallic        silver by the use of light or a photographic developer.    -   Other staining methods stain for example neutral lipids.        Preferably, this staining is used for the distinction between        fibroma and thekoma in the ovary. It further preferably used for        the diagnosis of renal cell carcinoma and sebaceous gland tumors        of the skin.

As already said, numerous staining methods are well known to thoseskilled in the art. Of course, also so far unknown methods may be usedaccording to the invention as long as they allow a determination ofcells of a subpopulation of cells.

In a preferred embodiment, the content of cells of a subpopulation ofcells is determined by means of staining methods which are based onspecific antibodies. Numerous suitable methods are well known to thosewith ordinary skills in the art. A rough overview could be gained fromthe following literature: Burck, H C. Histologische Technik: Leitfadenfür die Herstellung mikroskopischer Präparate in Unterricht and Praxis.6. edition, Thieme, 2002; Kiernan, J A. Histological and histochemicalmethods: theory and practice. 2. edition, Arnold Publishers, 1990;Ackermann, Rosai (editors). Surgical pathology. 9. edition, Mosby, 2004;Killeen, A A. Principles of Molecular Pathology. Humana Press, 2003;Romeis, B. Mikroskopische Technik. R. Oldenbourg Verlag, 1968 (all ofthese cited references are incorporated by reference to their entirety).But many more staining methods are known in the art and may be usedaccording to the invention. Of course, also so far unknown methods basedon specific antibodies may be used according to the invention as long asthey allow a determination of cells of a subpopulation of cells.

In a preferred embodiment, the cell content of a subpopulation of cellsis determined by means of antibody based stainings. The antibodies areused for the specific detection of antigens. They are either monoclonalantibodies or polyclonal antibodies. Furthermore they are produced indifferent animals: for example monoclonal antibodies in mouse andpolyclonal antibodies in rabbit, donkey, sheep or chicken. The detectionof the specifically bound antibody to an antigen may be achieved bydirect labeling of the antibody e.g. with a fluorescent dye. But also,and more commonly used, labeled bridging antibodies are used, whichspecifically bind to the constant region of the primary antibody. Inpreferred embodiments, the antibodies for detection are linked tofluorescent dyes which allow a specific detection by means of afluorescence microscope. Numerous of such fluorescent dyes are known tothose with ordinary skills in the art. In particular preferred are Cy2,Cy3 and/or Cy5. On overview of other suitable fluorescent dyes can beobtained form the “Fluorochrome Wall Chart” published by Zeiss (Germany;45-0033; hereby incorporated by reference in its entirety) or from thecorresponding internet page http://www.zeiss.de/mikro (herebyincorporated by reference in its entirety).

In another preferred embodiment, the antibodies for detection aremodified by linkage to additional enzymes, proteins, peptides orchemical substances which are allow the detection. These moleculesenable a detection of a specific antibody binding to an antigen by meansof a light microscope. In a particular preferred embodiment, thedetection may comprise the use of one or more of the following: biotin,avidin, horse reddish peroxidase, diaminobendzidin, and/or Envision.Numerous kits are available for the detection of antigen by means oflight microscopy. Companies who provide such kind of kits are forexample DAKO (Glostrup, DK) or Vector Labs (Burlingame, Calif., USA).But, of course other kits may also be used according to the invention.

According to the invention, any antibody can be used, specific for anyantigen, as long as it can be used for the determination of asubpopulation of cells.

A preferred embodiment is characterized in that the cell content of saidsubpopulation of cells is determined by using staining methods orspecific antibodies.

In a preferred embodiment, the cells of said subpopulation of cells aredisease-associated cells. In particular these cells might betumor-associated cells. Numerous methods are known to those withordinary skills in the art to identify a tumor-associated cell in atissue sample. For an rough overview please refer to Ackermann, Rosai(editors). Surgical pathology. 9. edition, Mosby, 2004 and to Killeen, AA. Principles of Molecular Pathology. Humana Press, 2003; herebyincorporated by reference in its entirety). Exemplary, tumor-associatedcell may be identified according to the following citeria: Cytologic orcytomophologic criteria of malignancy may be

a) polymorphism e.g. differences in the aspect of individual cells in atumor, up to giant nuclei that have the size of several normal nuclei;b) nuclear hyperchromasia e.g. increased nuclear uptake of Hematoxilin;c) an increased ration of nucleus to cytoplasm, interpreted as a sign ofincreased nuclear metabolic activity;d) prominent nucleolus, interpreted as a sign of increase nuclearsynthesis activity; ore) other cell morphologies or features, that are typically described forthe individual tumor, and often named after the first describer. Aperson with ordinary skills in the art knows these morphologies orfeatures for example, but not limited to the Reed-Sternberg cells inMobus Hodgkin, the Hodgkin cells in Morbus Hodgkin, the signet ring cellin gastric carcinoma, the lipoblasts in liposarcoma, the cristalloids inprostate carcinoma. Furthermore, so far unknown cell morphologies orfeatures are also preferred which will be discovered to be linked todisease-associated cells.

With regard to histologic criteria the main criteria of malignancy ofcells is infiltrative growth. This may vary depending on the tumor.Infiltration in epithelial tumor cells is often defined as growth beyondthe basal lamina. Tissues that show the cytologic criteria of malignancybut do not penetrate the basal lamina are called dysplasia. They arepre-neoplasias and have a high risk to become invasive, but they do notyet infiltrate and metastasize. An example is the cervicalintraepithelial neoplasia (CIN) a precessor of the squamous carcinoma ofthe cervix. Similar changes may be found in the larynx and the skin. Incontrast, urothelial papillary neoplasms are called carciomas also whenthey do not infiltrate beyond the basal lamina. Another criteria is thepresence of desmoplastic stroma. For example, colonic adenomas,precessors of colon carcinoma, do not display demoplastic stroma.However, infiltrative carcinomas, having developed within an adenoma,display fibroblastic proliferations (desmoplastic stroma) around theirglandules. In some lymphomas (e.g. MALT B cell lymphoma) malignancy maybe signified by the presence of lymphoid cells within the mucosaso-called lymphoepithelial lesions. Of course, the said are onlyexamples to which the subject matter of the invention is not limited.

Moreover malignant tumor cells may grow either in solid, glandular,cribriform, or single cell pattern, sometimes displaying also specialpatterns. These patterns are well known to those skilled in the art, forexample, but not limited to Homer-Wright-Rosettes in malignant peripherynerve sheath tumors or in undifferentiated neuroblastomas, orSchiller-Duval bodies in yolk-sack tumors, or Indian file pattern.Furthermore, significant cell morphologic changes over the area of thetumor as well as in the recurring tumor in comparison to the primarytumor are observeable.

A further histological citeria for malignancy of cells are blood andlymphatic vessel infiltration or growth beyond the tumor capsule forexample in follicular carcinoma of the thyroid gland.

In another preferred embodiment, disease-associated cells arespecifically detected by means of antigens associated with these cells.Suitable antigens or the corresponding antibodies for specific detectionare well known to those with ordinary skills in the art, for example,but not limited to pan cytokeratin antibodies such as AE1/AE3 (DAKO,Glosrup, DK)), antibodies usefull for the determination of proliferationrates such as MIB 1 antibodies (DAKO, Glosrup, DK), or antibodies whichdetect specific immunhistochemical markers. Antibodies of this purposemay be directed against cytoskeleton proteins, hormones, antigens of thelymphoreticular or hematopoetic system, oncofetal antigens, proteinaseinhibitors, viral and neural antigens, tissues and cell specificantigens, blood group antigens, or oncogene products. Of course,antibodies specific for other antigens even if they are so far unknowncan be used according to the invention as long as the are usefull fordetecting disease-associated cells.

A preferred embodiment is characterized in that the cell content of saidsubpopulation of cells is determined by histopathology.

In a preferred embodiment, the identified cells of said subpopulation ofcells, in particular the identified disease-associated cells, arecounted and the corresponding cell content is determined with referenceto the total amount of cells in a given area.

In a further preferred embodiment, the above said antibodies may be usedfor automatized cell counting. Several methods are known to thoseskilled in the art. Such methods are for example, but not limiting to amethod essentially carried out according to Demirkaya, O. et al. AnalQuant Cytol Histol. 1999 April; 21(2):93-102.; to Coon, J S. Lab Invest.1987; 57(5):453-79; to Sjöström, P J. et al. Cytometry. 1999,36(1):18-26; or to Xu, Y H. et al. Comput Methods Programs Biomed. 2000;63(1):55-70 (all of these cited references are incorporated by referenceto their entirety). According to these methods, cells of thesubpopulation of cells of interest are labeled immunohistochemicallywith one ore more antibodies and compared to all nuclei. The nuclearstain may be performed with DAPI (fluorescence detection) or withHematoxilin (detection by means of light microscopy). But also othersuitable nuclear stains are known to those skilled in the art andtherefore included herewith. Of course other so far unknown nuclearstains may be used according to the invention.

In another preferred embodiment, the FACS analysis is used. Thistechnique has the advantage that the cell content of a subpopulation ofcells of interest is directly determined with high accuracy. Varioussuitable methods are known those with ordinary skills in the art. Inbrief, the tissue sample has to be lysed to allow the preparation of acell suspension of single cells. The single cells are then labeledsubpopulation specifically with corresponding antibodies. Thereafter thelabeled cells are sorted and counted. The cell content of thesubpopulation of cells of interest is then determined by the ratio ofthe amount of cells of the subpopulation of cells of interest to theamount of the total cells.

In a preferred embodiment, the content of cells of a subpopulation ofcells is determined by using expression analysis. Such an analysis canbe any analysis method which determines quantitativ or semiquantitativethe amount of one or more proteins, peptides, RNAs or other chemicalcompounds which are specific for the said subpopulation of cells.Chemical compounds may be for example hormones or metabolic compounds.In principle, analysis methods may be used as already known to thoseskilled in the art, as well as so far unknown methods. In particular,analysis methods are preferred which are based on Western Blot analysis,Northern Blot analysis, Southern Blot analysis, ELISA, PCR, or DNAarrays. A person with ordinary skills in the art will know to choose anappropriate analysis method for expression analysis which is suitablefor determination of the cell content of a subpopulation of cells ofinterest.

In a preferred embodiment of the invention the cells of saidsubpopulation of cells are disease-associated cells. Such kind of cellsmay be detected by the detection of special chromosomal aberrationswithin cells. This aberrations may be for example, but not limited tobreakpoints, deletions, polysomias, or gene amplifications. They can bedetected for example by means of PCR, Southern Hybridisation, in situhybridisation, FISH analysis or CGH analysis. These methods are wellknown to those skilled in the art. Also oncogenic viruses like HPV orEBV may also be detected by means of FISH analysis or PCR.

A preferred embodiment of the invention is characterized in that thecell content of said subpopulation of cells is determined by usingexpression analysis.

In another preferred embodiment, the content of cells of a subpopulationof cells is determined by DNA methylation analysis. Thereby themethylation of one or more markers specific for one or moresubpopulations of cells is analysed. Such a marker may comprise one ormore CpG positions. In the simplest case the subpopulation of cellsspecific marker is a locus which comprises only a single CpG position.The DNA methylation at this single CpG position is then determinedquantitatively as already described in detail above. On the other side,the subpopulation of cells specific marker may comprise more than oneCpG position. If it is specific for the subpopulation of cells ofinterest that all CpG positions are methylated or unmethylatedsimultaneously, then it is sufficient to determine only the methylationof a single CpG position of the subpopulation of cells specific markerin a quantitative manner. Of course, it is also possible, and alsopreferred in other embodiments, to determine the DNA methylationquantitatively of a subset of CpG positions or of all CpG positions ofthe subpopulation of cells specific marker. In all three cases, thequantitative methylation is also determined as described above. However,in other embodiments more than one CpG position is comprised within thesubpopulation of cells specific marker and the different CpG positionsare methylated differentially. In this case, the methylation pattern ofthese CpG positions is determined which is specific for thesubpopulation of cells of interest in a quantitative manner. For this,several suitable methods are known to those skilled in the art.Preferably, bisulfite sequencing directly or after cloning of the DNAfragments, or primer extension are used.

In a preferred embodiment of the invention the determined methylation ofone or more subpopulation of cells specific markers is compared tovalues obtained from reference samples. The reference samples comprisecells of said subpopulation of cells and have a known cell content ofsaid cells.

A preferred embodiment of the invention is characterized in that thecell content of said subpopulation of cells is determined by DNAanalysis.

In a particular preferred embodiment the cell content of a subpopulationof cells of interest is determined from the total DNA amount and theamount of DNA which is methylated at one or more CpG positions of adefined locus. The methylation of said locus is thereby specific forsaid subpopulation of cells. Of course it is also possibly to considermore than one locus. In this case the results for the amount ofmethylated DNA and for the total DNA amount are each averaged. The ratioof the amount of methylated DNA to the total DNA amount represents thenthe cell content of the subpopulation of cells of interest in thesample.

In other particular preferred embodiments, it is specific for saidsubpopulation of cells that one or more cytosines at a defined locus areunmethylated. Also in this case it is possible to consider more than onelocus. For this, the results for the amount of unmethylated DNA and forthe total DNA amount are each averaged. The cell content of saidsubpopulation of cells is then represented by the ratio of thedifference between the total DNA amount and the amount of unmethylatedDNA to the total DNA amount.

A preferred embodiment is characterized in that the cell content of saidsubpopulation of cells is determined by

a) measuring, in one or more loci, the total DNA amount present in thetissue sample,b) measuring, in one or more loci, the amount of methylated DNA,c) determining the cell content of said subpopulation of cells in thetissue sample, as the amount of methylated DNA within the total DNA.

In particular preferred embodiment, the cell content of a subpopulationof cells of interest in determined from the total DNA amount and theamount of unmethylated DNA. Thereby it is specific for saidsubpopulation of cells that one or more cytosines at a defined locus areunmethylated. Of course it is also possibly to consider more than onelocus. In this case the results for the amount of unmethylated DNA andfor the total DNA amount are each averaged. The ratio of the amount ofunmethylated DNA to the total DNA amount represents then the cellcontent of the subpopulation of cells of interest in the sample.

In another particular preferred embodiment, the methylation of saidlocus is specific for said subpopulation of cells. The cell content ofsaid subpopulation of cells is then represented by the ratio of thedifference between the total DNA amount and the amount of unmethylatedDNA to the total DNA amount. Also in this case it is possible toconsider more than one locus. For this, the results for unmethylated DNAand for the total DNA amount are each averaged.

The total DNA amount of the above said embodiments is determinedaccording to standard techniques. Numerous methods are known to thoseskilled in the art. But also other, so far unknown methods are usable,which enable the determination of the amount of DNA.

A preferred embodiment of the invention is characterized in that thecell content of said subpopulation of cells is determined by

a) measuring, in one or more loci, the total DNA amount present in thetissue sample,b) measuring, in one or more loci, the amount of unmethylated DNA,c) determining the cell content of said subpopulation of cells in thetissue sample, as the amount of unmethylated DNA within the total DNA.

In particular preferred embodiment, the cell content of a subpopulationof cells of interest in determined from the amount of unmethylated DNAand the amount of methylated DNA. Thereby it is specific for saidsubpopulation of cells that one or more cytosines at a defined locus aremethylated. Of course it is also possibly to consider more than onelocus. In this case the results for the amount of unmethylated DNA andfor the total DNA amount are each averaged. The ratio of the amount ofmethylated DNA to the sum of the amount of unmethylated DNA and theamount of methylated DNA represents then the cell content of thesubpopulation of cells of interest in the sample.

In another particular preferred embodiment, it is specific for saidsubpopulation of cells that one or more cytosines at a defined locus areunmethylated. Also in this case it is possible to consider more than onelocus. For this, the results for the amount of unmethylated DNA and theamount for methylated DNA are each averaged. The cell content of saidsubpopulation of cells is then represented by the ratio of the amount ofunmethylated DNA to the sum of the amount of unmethylated DNA and theamount of methylated DNA.

A preferred embodiment of the invention is characterized in that thecell content of said subpopulation of cells is determined by

a) measuring, in one or more loci, the unmethylated DNA amount presentin the tissue sample,b) measuring, in one or more of said loci, the methylated DNA amountpresent in the tissue sample,c) determining the cell content of said subpopulation of cells of thetissue sample as the ratio of methylated DNA to unmethylated plusmethylated DNA, or as the ratio of unmethylated DNA to unmethylated plusmethylated DNA.

According to a further preferred embodiment, the ratio of the amount ofmethylated to the amount of unmethylated DNA is used for deducing thecell content of the subpopulation of cells of interest. This is inparticular preferred in cases in which it is favourable for technicalreasons to measure the ratio of methylated to unmethylated DNA or theratio of unmethylated to methylated DNA. A person with ordinary skill inthe art knows numerous possiblities how to deduce the cell content fromsaid ratios. For example, the cell content can be deduced by equatingthe amount of methylated DNA to the ratio of methylated to unmethylatedDNA and equating the amount of unmethylated DNA to 1. With theseequations it is possible to obtain the cell content according to theabove explained embodiments. On the other hand, it is also possible todeduce the cell content according to the above explained embodiments byequating the amount of unmethylated DNA to the ratio of unmethylated tomethylated DNA and equating the amount of methylated DNA to 1. Furtherpossibilities for deducing the cell content of a tissue sample are: i)comparing the ratio of methylated to unmethylated DNA of the tissuesample with the ratio of methylated to unmethylated DNA of a referencesample with known cell content; or ii) comparing the ratio ofunmethylated to methylated DNA of the tissue sample with the ratio ofunmethylated to methylated DNA of a reference sample with known cellcontent.

A further preferred embodiment of the invention is characterized in thatthe cell content of said subpopulation of cells is determined by

a) measuring, in one or more loci, the ratio of methylated DNA tounmethylated DNA present in the tissue sample, or by measuring, in oneor more loci, the ratio of unmethylated DNA to methylated DNA present inthe tissue sample, andb) determining the cell content of said subpopulation of cells of thetissue sample from the ratio of methylated DNA to unmethylated DNA, orfrom the ratio of unmethylated DNA to methylated DNA.

In a particular preferred embodiment, the cell content of asubpopulation of cells of interest in determined from the amount ofmethylated DNA and the total volume or the outer or total surface areaof the tissue sample. Thereby it is specific for said subpopulation ofcells that one or more cytosines at a defined locus are methylated. Inanother particular preferred embodiment, the cell content of asubpopulation of cells of interest in determined from the amount ofunmethylated DNA and the total volume or the outer or total surface areaof the tissue sample. Thereby it is specific for said subpopulation ofcells that one or more cytosines at a defined locus are unmethylated. Ofcourse, in both embodiments, it is also possibly to consider more thanone locus. In this case the results for the amount of methylated DNA andthe amount of unmethylated DNA are averaged, respectively. The ratiosobtained according to these embodiments are then compared with referencevalues from which the cell content of the subpopulation of cells ofinterest in the tissue sample can be deduced.

A preferred embodiment is characterized in that the cell content of saidsubpopulation of cells is determined by

a) measuring, in one or more loci, the amount of methylated DNA or theamount of unmethylated DNA present in the tissue sample,b) determining the cell content of said subpopulation of cells of thetissue sample, from the amount of methylated DNA and the total volume orsurface area of the tissue sample or from the amount of unmethylated DNAand the total volume or surface area of tissue sample.

In a particular preferred embodiment, the cell content of asubpopulation of cells of interest is deduced from the total DNA yieldobtained from a sample. Therefore the total DNA yield is compared withreference values from which the cell content of the subpopulation ofcells of interest in the tissue sample can be deduced. According to thisembodiment, the total DNA yield is thereby the total amount of DNA whichis normalized to the total volume or to the outer or total surface areaof the tissue sample. The DNA is thereby isolated and quantifiedaccording to standard techniques. Numerous possibilities are known tothose skilled in the art. Also so far unknown methods may be used whichare able to determine the total DNA yield.

A preferred embodiment of the invention is characterized in that thecell content of said subpopulation of cells is determined by measuringthe total DNA yield of a tissue sample in relation to the total volumeor the surface area of the tissue sample.

In a preferred embodiment of the invention the cells of the type ofinterest are disease-associated cells, wherein disease represents anykind of adverse events. In particular it represents at least onecategory selected from the group consisting of: undesired druginteractions; cancer diseases; CNS malfunctions; damage or disease;symptoms of aggression or behavioral disturbances; clinical;psychological and social consequences of brain damages; psychoticdisturbances and personality disorders; dementia and/or associatedsyndromes; cardiovascular disease of the gastrointestinal tract;malfunction, damage or disease of the respiratory system; lesion,inflammation, infection, immunity and/or convalescence; malfunction,damage or disease of the body as an abnormality in the developmentprocess; malfunction, damage or disease of the skin, of the muscles, ofthe connective tissue or of the bones; endocrine and metabolicmalfunction, damage or disease; and headaches or sexual malfunction. Inan especially preferred embodiment, the cells of the type of interestare associated with a proliferative disease, in particular with a cancerdisease. According to these embodiments, diseased tissue,disease-associated tissue, and/or healthy tissue are taken into accountfor the determination of the cell content.

In a preferred embodiment of the invention, the cells of saidsubpopulation of cells are disease-associated cells, preferably cellsassociated with a proliferative disease, in particular a cancer disease.

In a preferred embodiment, the total DNA methylation level and/or theamount of unmethylated DNA in one or more loci or the amount ofmethylated DNA in one or more loci is determined by means of bisulfitetreatment of the DNA derived from the tissue sample. Numerous methodsfor bisulfite treatment are known to those skilled in the art.

For example, but not limited to please refer to the said above. In aparticular preferred embodiment the bisulfite treatment is essentiallycarried out as described in WO05/038051 (this reference is incorporatedby reference in its entirety). Of course other, so far unknown methodsof bisulfite treatment may be used according to the invention as long asthe allow a subsequent measurement of the DNA methylation level, theamount of methylated DNA, and/or the amount of unmethylated DNA.

In preferred embodiment, the DNA derived from the tissue sample isbisulfite treated for the measurement of the total DNA methylationlevel, the measurement of the amount of methylated DNA, and/or themeasurement of the amount of unmethylated DNA.

In a preferred embodiment, the total DNA methylation level and/or theamount of unmethylated DNA in one or more loci or the amount ofmethylated DNA in one or more loci is determined by means of real-timePCR methods into which bisulfite treated DNA is subjected. Severalsuitable methods are known to those skilled in the art as alreadydescribed above. Of course, other so far unknown methods which are ableto detect DNA methylation quantitatively may be used.

A preferred embodiment of the invention is characterized in thatreal-time PCR is performed for measurement subsequent to bisulfitetreatment.

In a particular preferred embodiment, the total DNA methylation leveland/or the amount of unmethylated DNA in one or more loci or the amountof methylated DNA in one or more loci is determined by means of thereal-time PCR based methods MethyLight, MethyLight™ ALGO™, or the QM™assay. These methods are well known to those skilled in the art asalready described above. According to this embodiment bisulfite treatedDNA is subject to one or more of these methods.

A preferred embodiment of the invention is characterized in that theMethyLight™ method, the MethyLight™ ALGO™ method, or the QM™ assay isperformed for measurement subsequent to bisulfite treatment.

In a particular preferred embodiment, the total DNA methylation leveland/or the amount of unmethylated DNA in one or more loci or the amountof methylated DNA in one or more loci is determined by means of singlenucleotide primer extension, mini-sequencing or sequencing to each ofwhich bisulfite treated DNA is subjected. These methods are well knownto those skilled in the art. It is especially preferred that the primerextension is essentially carried out as described in Gonzalgo et al.(Nucleic Acids Research 25(12), 2529-2531, 1997), in U.S. Pat. No.6,251,594, in WO01/062960, in WO01/062064, or in WO01/62961 (all ofthese cited references are incorporated by reference to their entirety.

In brief, Gonzalgo et al. (Nucleic Acids Research 25(12), 2529-2531,1997), and U.S. Pat. No. 6,251,594 describe each a method for singlenucleotide primer extension also known as Ms-SNuPE (both of these citedreferences are incorporated by reference to their entirety). Accordingto the Ms-SNuPE method, regions of interest are amplified by PCR frombisulfite treated DNA. After purification of the PCR products, primersare proximately hybridized in front of the position to be anaylsed. Theprimer is then elongated by a single nucleotide either with labeled dCTPor with differently labeled dTTP. In case the cytosine in the originalDNA was methylated, then dCTP will be incorporated because methylatedcytosines remain unchanged during bisulfite treatment. In the othercase, the cytosine in the original DNA was unmethylated, then dTTP willbe incorporated because unmethylated cytosine is converted to uracil bybisulfite treatment and subsequent PCR will substitute uracil bythymine. By detection of the different labels, it can be distinguishedif a cytosine of a CpG position was methylated or unmethylated. TheMS-SNuPE method can also be performed in a quantitative manner.

Alternative methods for primer extension are described in WO01/062960,WO01/062064, or WO01/62961 all of which can be performed in aquantitative manner (all of these cited references are incorporated byreference to their entirety). According to WO01/062960, the primer to beextended hybridises with its 3′ terminus complete or only partially ontothe positions of interest. A extension of at least one nucleotide occursonly if the primer hybridises completely. WO01/062064 discloses analternative method in which the primer to be extended hybridisesproximately adjacent or at a distance of up to ten bases to the positionto be analysed. The primer is then extended by at least a singlenucleotide. The third alternative method is described in WO01/62961.According to this method, two set of oligonucleotides are hybridised tothe amplified DNA after bisulfite treatment. The first type ofoligonucleotide hybridises 5′ proximately adjacent or at a distance ofup to 10 bases to the position to be analysed. The second type ofoligonucleotide hybridises on the amplified DNA so that its 5′ terminushybridises 3′ proximately adjacent to said position to be analysed.Through this, the two oligonucleotide are separated from each other by agap of in the range of 1 to 10 nucleotides. The first type ofoligonucleotide is then extended by means of a polymerase, wherein notmore than the number of nucleotides lying between the twooligonucleotides are added. Thereby nucleotides are used which comprisedifferentially labeled dCTP and/or dTTP. The two oligonucleotides arethen linked to each other by means of a ligase enzyme. In case thecytosine in the original DNA was methylated, then dCTP will beincorporated. In case the cytosine in the original DNA was unmethylated,then dTTP will be incorporated.

It is further especially preferred that the results of themini-sequencing or sequencing of bisulfite treated DNA are essentiallyanalysed as described in EP 02090203.7 (hereby incorporated by referencein its entirety). In brief, according to this method the degree ofmethylation of a cytosine is determined by means of an electropherogramof one or more bases. Thereby the area underneath the electropherogramof a detected base is calculated. The degree of methylation is thendeduced by comparison this value for a cytosine position to be analysedwith the value obtained for an unmethylated cytosine. For betterresults, the determination and the consideration of the conversion rateof cytosine to uracil of the bisulfite treatment and/or astandardization of electropherogram signals is favourable.

A preferred embodiment of the invention is characterized in that singlenucleotide primer extension, mini-sequencing or sequencing is performedfor measurement subsequent to bisulfite treatment.

In a particular preferred embodiment, the total DNA methylation leveland/or the amount of unmethylated DNA or the amount of methylated DNA inone or more loci is determined by means of microarray hybridization.Suitable hybridisation methods are well known to those with ordinaryskills in the art. Such hybridization methods are described in detailfor example in WO01/38565 or WO02/18632 (both of these cited referencesare incorporated by reference to their entirety).

A preferred method of the invention is characterized in that microarrayhybridization is performed for measurement subsequent to bisulfitetreatment.

In a particular preferred embodiment, the total DNA methylation leveland/or the amount of unmethylated DNA in one or more loci or the amountof methylated DNA in one or more loci is determined by means ofmethylation specific restriction enzymes. Numerous suitable methods areknown to those with ordinary skills in the art. Preferably the Mestevaluation method or the DMH method is carried out. A person willordinary skills in the art knowns to carry out those methods. Forexample, but not limited to, the Mest evaluation method is described indetail in DE102004029700 (hereby incorporated by reference in itsentirety) and the DMH method is described in Huang et al. (Huang et al.,Hum Mol Genet, 8:459-470, 1999), in U.S. Ser. No. 09/497,855, in DE102005007185.6, in DE102005025 240.0, in DE102005036500.0, or in U.S.60/710,556 (all of these cited references are incorporated by referenceto their entirety). According to these, genomic DNA is fragmented byrestriction endonucleases before it is subject to a DNA microarray ofcloned CpG islands.

But, in a further preferred embodiment, the DMH method may also includeseveral improvements: After isolation of the DNA, an enrichment ofmethylated or unmethylated DNA takes place by different means. Thismeans can be one or more of the following: for example restrictionendonucleases or proteins, peptides or oligomers which specially bind toCpG dinucleotide either specific on methylated or on non-methylated CpGdinucleotides. Four variants of enrichment by means of restrictionendonucleases are especially preferred:

The enrichment by use of only methylation specific restriction enzymeswithout a previous addition of non-methylation specific restrictionenzymes but with a subsequent selective amplification of fragments inthe range of 50-5.000 bp via linker (also known as adapters by thoseskilled in the art). Preferred restriction enzymes are of the group“BisI, BstUI, BshI2361, AccII, BstFNI, McrBC, MvnI, HpaII (HapII), HhaI,AciI, SmaI, HinP1I, HpyCH4IV and mixtures of two or more of theaforesaid enzymes”.

Another enrichment is performed by at first, the restriction of DNA byone or more non-methylation specific restriction enzymes; secondly,fragments smaller than 50 bp are discarded and subsequently linker areligated on each end of every fragment; thirdly, the fragments providedwith linker are subject to a restriction by one or more methylationspecific restriction enzymes; and fourthly, the resulted fragments aresubjected to an amplification, wherein only fragments are amplifiedwhich are not restricted in step three. According to this procedurefragments of 50-5.000 bp are enriched. It is thereby preferably thatthree different methylation specific restriction enzymes are used, oneor more of the methylation specific restriction enzymes have arestriction site in the length of 4 bp, in particular which do notcontain any CG. The non-methylation specific restriction enzymes areselected from the group “MseI, BfaI, Csp6I, Tru1I, Tvu1I, Tru9I, Tvu9I,MaeI, XspI and mixtures of two or more of the aforesaid enzymes”.Preferably a mixture of MseI, BfaI and Csp6I is used. The methylationspecific restriction enzymes can be any enzyme which either cutsmethylation specifically unmethylated or methylated DNA. Preferably themethylation specific enzyme is selected from the group of “BisI, BstUI,BshI2361, AccII, BstFNI, McrBC, MvnI, HpaII (HapII), HhaI, AciI, SmaI,HinP1I, HpyCH4IV, EagI and mixtures of two or more of the aforesaidenzymes”. In particular the use of BstUI, HpaII, HpyCH4IV and HinP1I ispreferred.

Besides that, an enrichment is also possible according to the method of“NotI representation” as exemplified in WO02/086163 (hereby incorporatedby reference in its entirety). According to this, DNA is restricted bysuitable enzymes like BamHI of BglII. After inactivation of the enzymes,the fragments are circularized by self ligation, before they are subjectto another restriction by NotI which only cut its unmethylatedrecognition side. Through this, fragments with only unmethylated NotIrecognition sites are linearised onto which specific linker are ligated.Therefore it is possible to amplify those fragments. In principle thismethod can also be adjusted to other methylation specific restrictionenzymes as listed above.

As the fourth procedure of enrichment by the means of restrictionendonucleases, the MS AP-PCR (Methylation Sensitive Arbitrarily-PrimedPolymerase Chain Reaction) is preferred. This technique is well known inthe art and was described the first time by Gonzalgo et al., CancerRes., 57:594-599, 1997 (hereby incorporated by reference in itsentirety). In principle, genomic DNA is subject to an restrictiondigestion, for example HpaII. The resulting fragments are then subjectto an amplification wherein random primers are used which are rich in CGdinucleotides. According to this, DNA regions are amplified which arerich in CG dinucleotides.

An enrichment of methylated or non-methylated DNA can also occur bymeans of proteins, peptides or oligomers which specifically bind tomethylated or non-methylated DNA. The binding can be sequence specificor unspecific. However, unbound DNA is separated by bound DNA throughthe binding. Depending on which kind of DNA is of interest, methylatedor non-methylated DNA, or which kind of DNA is bound, the bound orunbound DNA fraction is further analysed. These means proteins may beused which specifically bind unmethylated DNA, as well as proteins whichspecifically bind methylated DNA. Furthermore, it is possible to bindthat DNA, which is later analysed. Therefore the unbound DNA is removedbefore the bound DNA is released from the protein. On the other hand itis also possible to let bind the background DNA to the proteins andthereby it is removed from the reaction mixture. Of course, it is alsopossible to carry out such an enrichment in two subsequent steps wherebythe order is not relevant. In one step, proteins which specifically bindunmethylated DNA and in the other step, proteins which specifically bindmethylated DNA are used. Such a proceeding has the advantage thatsimultaneously unmethylated DNA and methylated DNA are enriched whileDNA with no or only a view CpG positions is removed.

An enrichment can be achieved by proteins which methylation specificallybind to DNA and also by the use of their domains or peptides. Suchproteins can be for example MeCP2, MBD1, MBD2, MBD4 and Kaiso. The laterbinds sequence specifically namely on symmetrical methylated CpGpCpGpositions. Exemplary the Methyl-CpG-binding domain of MeCP2 protein orthe CXXC-3 domain of the MBD1 protein is mentioned as suitable domainsfor enrichment (for an overview: Shiraishi et al., Anal Biochem. 2004Jun. 1; 329 (1):1-10; Hendrich and Tweedie, Trends Genet. 2003 May, 19(5): 269-77; Jorgensen et al., Molecular and Cellular Biology, 2004,3387-3395; all of these cited references are incorporated by referenceto their entirety).

Typically, the proteins, domains or peptides are bound to a solidsurface for example on beads which enable a separation of by means of abatch procedure or by a column chromatography (Cross et al., NatureGenetics, 1994 (6) 236-244; Shiraishi et al., Anal Biochem. 2004 Jun. 1;329 (1):1-10; both of these cited references are incorporated byreference to their entirety). Biochemical methods which have to beapplied are known to those skilled in the art. This may for exampleinclude the use of biotin or histidine tags (for example Gretch et al.,Anal Biochem., 1987, (163) 270-7; Janknecht et al., Prc Nat. Acad Sci,1991, (88) 8972-6; both of these cited references are incorporated byreference to their entirety).

Moreover, an enrichment can also be achieved by methylation specificantibodies for example by means of the anti 5-methylcytosine antibodyavailable from Abcam Inc. Again the enrichment can be performed in abatch procedure or by column chromatography. Details are known topersons skilled in the art (for example: Fisher et al., Nucleic AcidsRes. 2004, 32(1), 287-97; hereby incorporated by reference in itsentirety). On the hand, an enrichment can also be achieved byimmunoprecipitation with methylation specific antibodies and suitablesecondary antibodies, followed by a proteinase K treatment.

Another variant of enrichment is the chromatin immunoprecipitation(ChIP). Details are known to those skilled in the art (for example:Matarazzo et al., Biotechniques, 2004, 37(4), 666-8, 670, 672-3.; herebyincorporated by reference in its entirety). According to this, aimmunoprecipitation is carried out with antibodies which are specificfor 5-methylcytosine binding proteins like MeCP2, MBD1, MBD2, MBD4 orKaiso. Thereby the proteins are fixed onto the DNA before the antibodiesare added. In particular it is preferred to purify the DNA first andthen add the DNA binding proteins. It is also particularly preferred toapply a suitable physical method like ultracentrifugation before thesecond precipitation step. A suitable kit is available from Panomics,Inc.

Furthermore, an enrichment can be achieved by triplex binding oligomers,which can PNA- or DNA-Oligomers. This method is described in detail inWO04/113564 (hereby incorporated by reference in its entirety). Inprinciple, a triplex-building oligomer is brought in contact with DNA.Thereafter it preferentially forms a triple helix with unmethylated DNAin comparison to methylated DNA. From this advantage is taken forenrichment.

In principle, a DNA may be fragmentated randomly or non-randomly beforeit is subject to enrichment by any method using proteins, peptides oroligomers. This is done as it is known by those skilled in the art.Fragmentation can be performed randomly for example with sonification orshearing. But is also can be performed non-randomly, preferentially bythe use of methylation specific restriction endonucleases, in particularof the group of “BisI, BstUI, BshI2361, AccII, BstFNI, McrBC, MvnI,HpaII (HapII), HhaI, AciI, SmaI, HinP1I, HpyCH4IV and any mixture of twoor more of the aforesaid enzymes”.

A further reduction of complexity can be achieved by physical methodswhich are applied before or after an amplification. Such physicalmethods can for example be gel electrophoresis, size-exclusionchromatography or filtration.

After enrichment of the DNA, the fragments are labelled preferentiallywith a suitable fluorescent dye. Such a dye enables selective one or twodimensional scanning. Typically Cy3 and/or Cy5 are used as dyes. Butalso other suitable dyes are known to those skilled in the art.Furthermore, it is preferred that the fragments are labelled withbiotin, which interacts with another substance in the actually detectionprocess. Thereby it is necessary to carry out two arrays which arecompared with each other.

The labelling is carried out preferentially by means of anamplification, in particular whole genome amplifications. Severalsuitable methods are known by those skilled in the art.

The labelled fragments are then subject to a DNA microarray which can beeither a array of cloned CpG islands or array of oligonucleotides. Theoligonucleotides of the oligonucleotide microarray can be anyoligonucleotide suitable for the detection of methylation ornon-methylation of CpG dinucleotides. Preferably the oligonucleotidesare design after fragments derived according to the following twostrategies:

According to the first strategy, A) the genome of an organism of desireis analysed for first fragments, which are flanked by recognition sitesof non-methylation specific restriction enzymes of interest and whichare in the range of 100-1.200 bp. B) Second fragments are then selectedunder those first fragments which have no more than 50%, preferably nomore than 20% of repeats. These two steps A) and B) can be performed inarbitrary order. Additionally, C) the second selected fragments areanalysed for the presence of recognition sites of methylation specificrestriction endonucleases of interest.

Those second fragments which include such a recognition site are thenselected as third fragments. Again, the steps A), B) and C) can beperformed in arbitrary order.

According to the second strategy, A) the genome of an organism of desireis analysed for first fragments, which are flanked by recognition sitesof methylation specific restriction enzymes of interest and which are inthe range of 100-1.200 bp. B) Second fragments are then selected underthose first fragments which have no more than 50%, preferably no morethan 20% of repeats. C) The second selected fragments are analysed forthe presence of recognition sites of methylation specific restrictionendonucleases of interest. Those second fragments which include such arecognition site are then selected as third fragments. Again, the stepsA), B) and C) can be performed in arbitrary order.

According to the third strategy, A) the genome of an organism is testedfor first partial sequences, which are limited by cutting sites of oneor several of the first used restriction enzymes and have a length of100 to 1,200 base pairs, and said first partial sequences are selected,B) such partial sequences are excluded from the first partial sequences,which comprise more than 50% repeats—it is preferred, if such partialsequences are excluded, which contain more than 20% repeats, thereby agroup of second partial sequences being formed, and the steps A) and B)can be performed in any order, C) the selected second partial sequencesare tested for cutting sites of the restriction enzymes used secondly,and as third partial sequences those second partial sequences areselected, which contain such cutting sites, and the steps A) to C) canbe performed in any order.

Fragments selected according to these strategies can match fragmentsobtained by the enrichment procedures. The sequence of theoligonucleotides of the array is chosen from the selected fragments, sothat they would hybridise to the selected fragments or so that they areidentical to them and therefore would hybridise to the counter strand.These oligonucleotides are then synthesised on the array or are linkedto it after the synthesis. Typically 3-30 oligonucleotides are derivedfrom one fragment, whereby it is possible that the oligonucleotidesequences are overlapping. Preferably the oligonucleotides have adefined distance between each other so that a so called “tiling array”results, similar as described by Kapranov et al., Science, 2002,296(5569):916-9; hereby incorporated by reference in its entirety).

According to the DMH method, fragments hybridized on the immobilizedoligonucleotides contain preferably nucleic acid sequences, whichmethylation positions are non-methylated or methylated in case of adefinite disease in comparison to the normal condition. Theoligonucleotides do not have to necessarily encode for the methylationpositions by themselves, although it is possible. Moreover, it ispossible that a oligonucleotide array carries different sets ofoligonucleotides, suitable for the detection of different diseases or ofpredispositions for a disease or of the susceptibility for side effectsfor a definitive medical treatment. Additionally, it is also possible topredict the type, the aggressiveness or the progression of a disease orfor the effectiveness of a medical treatment, in case it is based onmethylation differences. Further conclusions can be made by comparisonof the results obtained by means of an oligonucleotide array accordingto the DMH method with a results obtained with arrays with differentoligonucleotide set, for example oligonucleotide sets suitable for SNPanalysis.

A preferred embodiment of the invention is characterized in that thetotal DNA methylation level, the amount of methylated DNA, and/or theamount of unmethylated is measured using methylation specificrestriction enzymes, preferably the Mest evaluation method or the DMHmethod.

Of course, also so far unknown methods may also used for thedetermination of the total DNA methylation level and/or the amount ofunmethylated DNA or the amount of methylated DNA in one or more loci.

A preferred embodiment of the invention is a method for diagnosing acondition or a disease. The condition or disease is therebycharacterized by methylation levels at one or more CpG dinucleotides,the levels and positions are specific for said condition or disease.Furthermore this embodiment comprises, a) obtaining a tissue sample withdisease-associated cells, b) determining the content of thedisease-associated cells within said tissue sample, c) measuring themethylation levels at one or more CpG dinucleotides within thedisease-associated cells from the total DNA methylation level and thedisease-associated cell content, and e) comparing said methylation levelat one or more CpG dinucleotides within the disease-associated cells toa corresponding reference value.

A preferred embodiment of the invention is method for diagnosing acondition or disease, characterized by specific methylation levels ofone or more methylation variable genomic DNA positions in adisease-associated cell of a tissue sample, comprising:

a) obtaining a tissue sample comprising genomic DNA having one or moremethylation variable positions in one or more regions thereof,b) determining the disease-associated cell content within the tissuesample in a quantitative or semi-quantitative manner,c) measuring the total DNA methylation level of one or more methylationvariable genomic DNA positions of the tissue sample,d) determining the DNA methylation level of one or more methylationvariable genomic DNA positions within the disease-associated cells fromthe total DNA methylation level and the disease-associated cell content,e) comparing said methylation level to that of corresponding referencetissue.

Another preferred embodiment is a method for predicting treatmentresponse or prognosis of disease for an individual. The treatmentresponse, the disease and/or the health status of the individual arecharacterized by methylation levels at one or more CpG dinucleotides,the levels and methylation positions are hereby specific for saidtreatment response, disease or health status. In addition, thisembodiment comprises, a) obtaining a tissue sample withdisease-associated cells from said individual, b) determining thecontent of the disease-associated cells within said tissue sample, c)measuring the methylation levels at one or more CpG dinucleotides withinthe disease-associated cells from the total DNA methylation level andthe disease-associated cell content, and e) comparing the methylationlevel at one or more CpG dinucleotides specific for the health status ofthe individual to a corresponding reference value which is specific forthe treatment response or the disease.

A preferred embodiment of the invention is a method for predictingtreatment response or prognosis of disease for an individual,characterized by specific methylation levels of one or more methylationvariable genomic DNA positions in a disease-associated cell of a tissuesample, comprising:

a) obtaining a tissue sample comprising genomic DNA having one or moremethylation variable positions in one or more regions thereof,b) determining the disease-associated cell content within the tissuesample in a quantitative or semi-quantitative manner,c) measuring the total DNA methylation level of one or more methylationvariable genomic DNA positions of the tissue sample,d) determining the DNA methylation level of one or more methylationvariable genomic DNA positions within the disease-associated cells fromthe total DNA methylation level and the disease-associated cell content,e) comparing said methylation level to that of corresponding referencetissue.

Subject of the present invention is also kit, comprising

a) reagents for quantitative or semiquantitative determination of thecell content of a subpopulation of cells within a tissue sample,b) reagents for measuring the total DNA methylation level of one or morespecific CpG positions of said subpopulation of cells within the tissuesample, andc) a container.

Preferably, a kit according to the invention comprises

-   -   a container.    -   one or more reagents for quantitative or semi-quantitative        determination of the cell content of a subpopulation of cells of        interest within a tissue sample. Said reagent may be any        substance, solution or device which is suitable for the above        said determination of the cell content according by means of        histopathology, staining or specific antibodies. Suitable        substances, solutions, or devices are well known to those        skilled in the art.

Furthermore, the said reagent may be any substance, solution or devicesuitable for carrying out a expression analysis as said above. Suitablesubstances, solutions, or devices are well known to those skilled in theart. In addition, the said reagent may also be any substance, solutionor device suitable for carrying out a DNA methylation analysis, inparticular by means of bisulfite treatment, the MethyLight™ method, theMethyLight™ ALGO™ method, the QM™ assay, nucleotide primer extension,mini-sequencing, sequencing, hybridisation on DNA microarrays,hybridisation on oligomer arrays, methylation-specific restrictionenzymes, the Mest evaluation method, the DMH method, or all of theaforesaid or only parts thereof as said above. Suitable substances,solutions, or devices are well known to those skilled in the art.

-   -   one or more reagents for the quantification of the total DNA        methylation level at one or more specific CpG positions within        the cells of a subpopulation of cells of interest. Said reagent        may be any substance, solution or device for carrying out the        DNA methylation analysis as it was already mentioned above.

Another preferred kit comprises, in addition, instructions or algorithmsfor carrying out the method of the invention. Such kind of instructionsor algorithms may comprise information how to determine the methylationlevel within cells of a subpopulation of cells of a given tissue sample.

In addition, a preferred kit of the invention comprises

a) reagents for quantitative or semiquantitative determination of thecell content of a subpopulation of cells within a tissue sampleb) reagents for measuring the total DNA methylation level of one or morespecific CpG positions of said subpopulation of cells within the tissuesample,c) a container, andd) operator instructions and/or algorithms to determine the methylationlevel within the cells of a subpopulation of cells of a given sample.

A particular preferred kit comprises furthermore one or more of thefollowing

a) one or more solution and/or reagent for histological and/orimmunological analysis,b) one or more primer and/or solution for DNA amplification, andc) one or more primer, oligonucleotide and/or solution for detection ofthe DNA methylation level and/or the detection of the amount ofmethylated and/or unmethylated DNA.

Another preferred kit of invention comprises one or more of thefollowing:

-   -   a container,    -   one or more primer suitable for the amplification of a        subpopulation of cells specific DNA methylation marker to        determine the cell content of said subpopulation of cells,    -   one or more primer suitable for the amplification of one or more        fragments to determine the DNA methylation level of one or more        specific CpG positions within the total DNA, and    -   operator instructions and/or algorithms to determine the        methylation level within the tumor cells of a given sample.

Preferably, the said kits are kits suitable for conducting a method oran embodiment of the invention.

The embodiments and kits disclosed herein are preferably used for theanalysis, characterization, classification, differentiation, grading, orstaging of cells or combinations thereof. Preferably these cells aredisease associated, in particular these cells are tumor cells. From suchan analysis, characterization, classification, differentiation, grading,staging or combinations thereof a person with ordinary skills in the artcan deduce an analysis, characterization, classification,differentiation, grading, staging or combinations thereof from adiseased tissue. A person with ordinary skills in the will then be ableto diagnose a proliferative disorder, a predisposition to such aproliferative disorder or a combination of both.

Preferably, the methods and kits described herein are used for analysis,characterization, classification, differentiation, grading, staging of acell or tissue, diagnosis of proliferative disorders, diagnosis of thepredisposition to proliferative disorders, or combinations thereof.

Of course, in the same manner also indication-specific targets can beidentified which are specific for a predisposition for a disease orwhich are specific for a progression of a disease.

The use according to one or more of the embodiments or of a kitaccording to the invention is preferred for identifying anindication-specific target, wherein

a) the DNA methylation level in disease-associated cells of asubpopulation of cells within a tissue sample is determined,b) the DNA methylation level in corresponding healthy cells isdetermined; andc) a indication-specific target is defined based on differences in theDNA methylation level of the DNA derived from the disease-associatedcells in comparison to the DNA derived from the corresponding healthycells.

The use of the methods or kits described herein is preferred if theindication-specific target is a protein, peptide, RNA or any otherendogeneous bioactive substance as for example a hormon.

The use is preferred if the indication specific target is a protein,peptide or RNA.

In particular, a use is preferred wherein a per se known modulator ofthe protein, peptide or RNA is assigned to the specific indication ofthe diseased tissue.

Furthermore, the use of such a modulator is particularly preferred forpreparing a pharmaceutical composition in case of a specific indication.This is especially preferred if the specific indication is a specificcancer indication.

In particular, the use of the modulator assigned to the specificindication of the diseased tissue is preferred for preparing apharmaceutical composition with a specific indication, in particular aspecific cancer indication.

The methods and kits disclosed herein are preferable used for diagnosis,prognosis or both of adverse events of patients or individuals. Therebydiagnosis means diagnose of a adverse event, a predisposition for anadverse event and/or a progression of a adverse events. Furthermoreprognosis means prognose of a adverse event, a predisposition for aadverse event and/or a progression of a adverse events. These adverseevents belong at least to one of the following categories: undesireddrug interactions; cancer diseases; CNS malfunctions; damage or disease;symptoms of aggression or behavioral disturbances; clinical;psychological and social consequences of brain damages; psychoticdisturbances and personality disorders; dementia and/or associatedsyndromes; cardiovascular disease of the gastrointestinal tract;malfunction, damage or disease of the respiratory system; lesion,inflammation, infection, immunity and/or convalescence; malfunction,damage or disease of the body as an abnormality in the developmentprocess; malfunction, damage or disease of the skin, of the muscles, ofthe connective tissue or of the bones; endocrine and metabolicmalfunction, damage or disease; and headaches or sexual malfunction.

The methods and test kits disclosed herein are also preferably used fordistinguishing subpopulations of cells, tissues or for investigatingcell differentiation. In a preferred embodiment, this information may beused for analysing the response of a patient to a drug treatment.

All cited references are hereby incorporated by reference in theirentirety.

Example 1 Methylation Markers Analysis of Biological Samples ComprisingLung Cancer

The aim of the present example was to establish that the methodaccording to the present invention was suitable for analysis ofbiological samples in order to quantify the amount of cancer cells. Lungcancer was selected as a first case study.

In order to quantifying the amount of lung cancer cells in a biologicalsample, as relative to the amount of normal lung cells according to themethod of the present invention it was first necessary to determinemethylation markers suitable for differentiating between normal lungtissue and lung cancer tissue, wherein said lung cancer tissue is notcontaminated by other cell types. Accordingly lung cancer cell lineswere used as immortalized cell lines are solely comprised ofproliferating cells do not comprise normal tissues. Furthermore in orderto confirm that the selected methylation markers were heterogeneouslymethylated in lung cancer samples, the methylation patterns thereof werealso determined in biopsy samples from lung cancer patients.

Suitable methylation markers were identified by means of a differentialmethylation hybridisation investigation of lung normal tissue, lungcancer cell lines & lung cancer biopsy. Differential methylationhybridisation was carried out substantially as described by Huang etal., Hum Mol Genet, 8 (3): 459-470 (1999).

Samples

20 tissue samples from healthy lung, 22 surgically removed lung cancersamples and 9 lung cancer cell lines (taken from the NCBI 60 panel ofcell lines) were analysed. The surgically removed lung cancer sampleshad previously been assessed by a pathologist to determine % tumourcontent of the sample.

Furthermore, artificially ss1 methylated (100% methylation) DNA andcommercially available unmethylated genomic DNA (0% methylation) DNAwere also analysed as controls. This enabled calibration of the results.

Differential Methylation Hybridisation DNA Isolation

Genomic DNA was isolated by means of the QIAamp DNA Mini Kit (Qiagen,Hilden, Germany) in accordance with the manufacturer's instructions.

2: Generation of DNA-Microarrays with Oligonucleotides

A whole genome DNA microarray was designed by in-silico analysis of theEnsemble Human Genome database to determine restriction fragments bydigestion with selected restriction enzymes, both methylation specificand non-methylation specific.

A subset of the possible restriction fragments was then selected usingcriteria that included but were not limited to fragment size, repeatcontent.

Said selected subset of fragments was then synthesised on a microarraysurface according to conventional means.

3: Restriction Digest of the DNA Samples

The genomic DNA was prepared for hybridisation to the microarray.

Genomic DNA of each sample was first digested with non-methylationspecific restriction enzymes MseI, Bfa1 and Csp6 (obtainable from NewEngland Biolab and MBI Fermentas) according to the manufacturer'sinstructions. Purification was then performed with the QuiaQuick PCRproduct purification column kit (Quiagen, Hilden, Germany). Fragmentsshorter than 40 bases were rejected according to the manufacturersinformation. However it cannot be excluded that larger fragments up to asize of about 100 bp also rejected. Subsequently, the ligation ofadapters (or linkers) was performed according to the procedure describedby Huang et al., Hum Mol Genet, 8 (3): 459-470 (1999). After this, thepurified ligated DNA was digested with 10 units each of the methylationsensitive (i.e. methylation specific) restriction enzymes BstU1, Hap II,HpyCH4iV and HinP1 (obtainable from New England Biolabs) according tothe manufacturers instructions.

About 10-100 ng of the methylation sensitive digested DNA was used for aPCR reaction, which amplifies unrestricted DNA fragments in the range of50-1000 bp. The amplified DNA was purified by means of the QuiaQuick PCRproduct purification kit (Qiagen, Hilden, Germany).

The purified PCR products were fragmented and labeled according to thespecifications of the “Gene Chip Mapping Assay Manual” of AffymetrixInc., in particular Chapter 4 (pages 38-42).

4: Hybridisation of Samples on the DNA Microarray

The amplificates hybridised to the DNA microarray synthesised as above.The hybridisation and detection was carried out according to theinstructions in “Gene Chip Mapping Assay Manual” by Affymetrix Inc., inparticular chapter 5 (page 69-70), as well as chapter 6 “Washing,Staining & Scanning” (page 75-92).

Each sample thereby generated an individual hybridisation pattern, fromwhich methylation differences between the three sample types could bededuced by determining DNA fragment sequences which show differentialhybridisation signals between samples of the compared tissues.

Results

FIGS. 1 and 2 together provide an overview of the relative methylationof approximately 1,000 fragments of the DMH chip.

Each column of the matrices represent the DMH methylation data for onesample. Each row of a matrix represents a DMH fragment and each columnrepresents an individual DNA sample. The degree of methylationrepresented by the shade of each position within the column from blackrepresenting 100% methylation to light grey representing 0% methylation.The degree of methylation was determined by calibration to the 0% and100% methylated controls. Fragments are ranked in the matrix accordingto the difference in average methylation between the normal and lungcancer tissue (not cell line) groups.

Based on a threshold of 25% methylation difference 497 fragments wereidentified which were generally hypermethylated in cell lines (FIG. 1),and 556 that were generally hypomethylated in cell lines (FIG. 2). InFIG. 1 fragments with the highest difference in average methylationbetween the normal and lung cancer tissue (not cell line) groups arelisted at the top of the matrix. In FIG. 2 fragments with the highestdifference in average methylation between the normal and lung cancertissue (not cell line) groups are listed at the bottom of the matrix.

In each of FIGS. 1 and 2 the different groups of samples are presentedin a discreet block. “A” indicates normal tissue, “B” indicatessurgically removed lung cancer samples and “C” indicates lung cancercell lines.

It can be seen that many fragments are capable of differentiatingbetween lung normal tissue and lung cancer cell lines such that they aresubstantially 100% methylated in one class and substantially 0%methylated in the other class. It can be further concluded that thesurgically removed lung cancer samples generally present with a mixeddegree of methylation as compared to the cell lines. Accordingly 40markers were selected, namely the lower 20 markers which werehypomethylated in cell lines from FIG. 2 (referred to in FIG. 3 as“hypomethylated”), and the first 20 markers which were hypermethylatedin lung cell lines and hypomethylated in lung normal tissues from FIG. 1(referred to in FIG. 3 as “hypomethylated”). The sequence of each ofsaid genomic nucleic acid fragment is provided in the sequence listing.SEQ ID NO: 1 to SEQ ID NO: 20 provide the sequences of the markers whichwere hypomethylated in cell lines. SEQ ID NO: 21 to SEQ ID NO: 40provide the sequences of the markers which were hypermethylated in celllines.

20 of the surgically removed lung cancer samples were then selected. Foreach of the samples the average quantified methylation of the 20fragments in each of the hypomethylated and hypermethylated groups wasdetermined. The average of the each was then plotted against each other,as shown in FIG. 3. The correlation of the plot was −0.571.

The methylation average methylation values of the hypo- andhyper-methylated groups of fragments was then plotted against the tumourcell content of each sample, as estimated by a pathologist. FIG. 4 showsthe plot of hypomethylated average against % tumour cell content, thecorrelation of the plot was −0.329. FIG. 5 shows the plot ofhypomethylated average against % tumour cell content, the correlation ofthe plot was −0.456.

1. Method for the determination of the DNA methylation level of one or more specific CpG positions of a subpopulation of cells within a tissue sample, comprising a) determining the cell content of said subpopulation of cells within the tissue sample in a quantitative or semi-quantitative manner, b) measuring the total DNA methylation level of said one or more specific CpG positions within the tissue sample, c) determining the DNA methylation level within the cells of said subpopulation of cells from the total DNA methylation level of said one or more specific CpG positions within the tissue sample and the cell content of said subpopulation of cells within the tissue sample.
 2. Method according to claim 1, characterized in that the cell content of said subpopulation of cells is determined by using staining methods or specific antibodies.
 3. Method according to claim 1, characterized in that the cell content of said subpopulation of cells is determined by histopathology.
 4. Method according to claim 1, characterized in that the cell content of said subpopulation of cells is determined by using expression analysis.
 5. Method according to claim 1, characterized in that the cell content of said subpopulation of cells is determined by DNA methylation analysis.
 6. Method according to claim 5, characterized in that the cell content of said subpopulation of cells is determined by a) measuring, in one or more loci, the total DNA amount present in the tissue sample, b) measuring, in one or more loci, the amount of methylated DNA, c) determining the cell content of said subpopulation of cells in the tissue sample, as the amount of methylated DNA within the total DNA.
 7. Method according to claim 5, characterized in that the cell content of said subpopulation of cells is determined by a) measuring, in one or more loci, the total DNA amount present in the tissue sample, b) measuring, in one or more loci, the amount of unmethylated DNA, and c) determining the cell content of said subpopulation of cells in the tissue sample, as the amount of unmethylated DNA within the total DNA.
 8. Method according to claim 5, characterized in that the cell content of said subpopulation of cells is determined by a) measuring, in one or more loci, the unmethylated DNA amount present in the tissue sample, b) measuring, in one or more of said loci, the methylated DNA amount present in the tissue sample, and c) determining the cell content of said subpopulation of cells of the tissue sample as the ratio of methylated DNA to unmethylated plus methylated DNA, or as the ratio of unmethylated DNA to unmethylated plus methylated DNA.
 9. Method according to claim 5, characterized in that the cell content of said subpopulation of cells is determined by a) measuring, in one or more loci, the ratio of methylated DNA to unmethylated DNA present in the tissue sample, or by measuring, in one or more loci, the ratio of unmethylated DNA to methylated DNA present in the tissue sample, and b) determining the cell content of said subpopulation of cells of the tissue sample from the ratio of methylated DNA to unmethylated DNA, or from the ratio of unmethylated DNA to methylated DNA.
 10. Method according to claim 5, characterized in that the cell content of said subpopulation of cells is determined by a) measuring, in one or more loci, the amount of methylated DNA or the amount of unmethylated DNA present in the tissue sample, b) determining the cell content of said subpopulation of cells of the tissue sample, from the amount of methylated DNA and the total volume or surface area of the tissue sample or from the amount of unmethylated DNA and the total volume or surface area of tissue sample.
 11. Method according to claim 1, characterized in that the cell content of said subpopulation of cells is determined by measuring the total DNA yield of a tissue sample in relation to the total volume or surface area of the tissue sample.
 12. Method according to claim 1, wherein the cells of said subpopulation of cells are disease-associated cells, preferably cells associated with a proliferative disease, in particular a cancer disease.
 13. Method according to claim 1, wherein DNA derived from the tissue sample is bisulfite treated for the measurement of the total DNA methylation level, the measurement of the amount of methylated DNA, and/or the measurement of the amount of unmethylated DNA.
 14. Method according to claim 13, characterized in that real-time PCR is performed for measurement subsequent to bisulfite treatment.
 15. Method according to claim 14, characterized in that the MethyLight™ method, the MethyLight™ ALGO™ method, or the QM™ assay is performed for measurement subsequent to bisulfite treatment.
 16. Method according to claim 13, characterized in that single nucleotide primer extension, mini-sequencing or sequencing is performed for measurement subsequent to bisulfite treatment.
 17. Method according to claim 1, characterized in that microarray hybridization is performed for measurement subsequent to bisulfite treatment.
 18. Method according to claim 1, characterized in that the total DNA methylation level, the amount of methylated DNA, and/or the amount of unmethylated is measured using methylation specific restriction enzymes, preferably the Mest evaluation method or the DMH method.
 19. Method for diagnosing a condition or disease, characterized by specific methylation levels of one or more methylation variable genomic DNA positions in a disease-associated cell of a tissue sample, comprising: a) obtaining a tissue sample comprising genomic DNA having one or more methylation variable positions in one or more regions thereof, b) determining the disease-associated cell content within the tissue sample in a quantitative or semi-quantitative manner, c) measuring the total DNA methylation level of one or more methylation variable genomic DNA positions of the tissue sample, d) determining the DNA methylation level of one or more methylation variable genomic DNA positions within the disease-associated cells from the total DNA methylation level and the disease-associated cell content, e) comparing said methylation level to that of corresponding reference tissue.
 20. Method for predicting treatment response or prognosis of disease for an individual, characterized by specific methylation levels of one or more methylation variable genomic DNA positions in a disease-associated cell of a tissue sample, comprising: a) obtaining a tissue sample comprising genomic DNA having one or more methylation variable positions in one or more regions thereof, b) determining the disease-associated cell content within the tissue sample in a quantitative or semi-quantitative manner, c) measuring the total DNA methylation level of one or more methylation variable genomic DNA positions of the tissue sample, d) determining the DNA methylation level of one or more methylation variable genomic DNA positions within the disease-associated cells from the total DNA methylation level and the disease-associated cell content, e) comparing said methylation level to that of corresponding reference tissue.
 21. Kit, comprising a) reagents for quantitative or semiquantitative determination of the cell content of a subpopulation of cells within a tissue sample, b) reagents for measuring the total DNA methylation level of one or more specific CpG positions of said subpopulation of cells within the tissue sample, and c) a container.
 22. Kit of claim 21, comprising operator instructions and/or algorithms to determine the methylation level within the tumor cells of a given sample.
 23. Kit of claim 21 comprising one or more of the following a) one or more solution and/or one or more reagent for histological and/or immunological analysis, b) one or more primer and/or one or more solution for DNA amplification, and c) one or more primer, one or more oligonucleotide and/or one or more solution for detection of the DNA methylation level and/or the detection of the amount of methylated and/or unmethylated DNA.
 24. Kit, comprising one or more of the following: a container, one or more primer suitable for the amplification of a subpopulation of cells specific DNA methylation marker to determine the cell content of said subpopulation of cells, one or more primer suitable for the amplification of one or more fragments to determine the DNA methylation level of one or more specific CpG positions within the total DNA, and operator instructions and/or algorithms to determine the methylation level within the tumor cells of a given sample.
 25. Kit according to claim 21 for conducting a method according to one of the preceeding claims.
 26. Use of a method according to claim 1 for analysis, characterization, classification, differentiation, grading, staging of a cell or tissue, diagnosis of proliferative disorders, or the predisposition to proliferative disorders, or combinations thereof.
 27. Use of a method according to claim 1 for identifying an indication-specific target, wherein a) the DNA methylation level in disease-associated cells of a subpopulation of cells within a tissue sample is determined, b) the DNA methylation level in corresponding healthy cells is determined; and c) a indication-specific target is defined based on differences in the DNA methylation level of the DNA derived from the disease-associated cells in comparison to the DNA derived from the corresponding healthy cells.
 28. Use according to claim 27, wherein the indication-specific target is a protein, peptide or RNA.
 29. Use according to claim 28, wherein a per se known modulator of the protein, peptide or RNA is assigned to the specific indication of the diseased tissue.
 30. Use of the modulator assigned according to claim 29 for preparing a pharmaceutical composition in case of a specific indication, or a specific cancer indication.
 31. Use of the method according to claim 1 for diagnosis, prognosis or both of adverse events for patients or individuals, wherein the adverse events comprise at least one category selected from the group consisting of: undesired drug interactions; cancer diseases; CNS malfunctions; damage or disease; symptoms of aggression or behavioral disturbances; clinical; psychological and social consequences of brain damages; psychotic disturbances and personality disorders; dementia and/or associated syndromes; cardiovascular disease of the gastrointestinal tract; malfunction, damage or disease of the respiratory system; lesion, inflammation, infection, immunity and/or convalescence; malfunction, damage or disease of the body as an abnormality in the development process; malfunction, damage or disease of the skin, of the muscles, of the connective tissue or of the bones; endocrine and metabolic malfunction, damage or disease; and headaches or sexual malfunction.
 32. Use of the method according to claim 1 for distinguishing subpopulations of cells or tissue or for investigating cell differentiation. 